The federal subpoenas means SeaWorld will continue to be mired in the scandal that arose over the documentary, despite taking steps to distance itself from some of the practices that were the target of the film.
Blackfish, the documentary released in 2013, led activists to believe that SeaWorld was keeping killer whales in small tanks, instead of bigger pens at sea.
The two investigations are probing into public statements and disclosures made by executives at the company in August of 2014 or earlier that were related to the impact of the documentary "Blackfish" and shares of SeaWorld, according to one of the company's public filings.
SeaWorld said that it has put together a special committee that will work towards complying with the federal investigations, proving the company's innocence.
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In the filing where SeaWorld disclosed the investigation, the company also revealed news about a more recent issue.
SeaWorld shares fell 33 per cent on a single day in August 2014, when the theme-park operator reported earnings that missed analysts" estimates and blamed the scrutiny of its treatment of animals in the wake of CNN's "Blackfish', which was released in 2013.
SeaWorld's new leadership - CEO Joel Manby was hired in 2015 - has been eager to refocus attention on new rides, family friendly attractions, and rescue work by staffers.
Reached by email, the SEC and Justice Department declined to comment late Friday. PETA claims SeaWorld's animals live shorter lives in captivity than they would in the wild. It details the alleged mistreatment by workers at SeaWorld of its orca whales, and led to huge backlash from different groups and organizations.
Last year, SeaWorld announced that the killer whales now in its care will be the last generation of the mammals enclosed at the water parks.